BIOMOLECULES AND CELLS:

BIO 111
Mr. Derrick Banda MSc, BSc
 LECTURE 3:CHEMICAL BONDS AND
FUNCTIONAL GROUPS IN BIOMOLECULES
 Introduction to Chemical Bonds
• Chemical Bonding refers to connections between two or more atoms,
molecules, or ions to give rise to a chemical compound.
• These chemical bonds are what keep the atoms together in the
resulting compound.

• These bonds include both strong intramolecular interactions, such as

covalent and ionic bonds.

• They are also related to weaker intermolecular forces, such as

hydrogen bonding, van der Waals (London dispersion) interactions and
dipole-dipole interactions.
 Introduction to Chemical Bonds
• All chemical reactions involve breaking of some bonds and formation of
new ones which yield new products with different properties.

• The properties of substances are determined in large part by the

chemical bonds that hold their atoms together
 Lewis Theory of Chemical Bonding
• Atoms ONLY come together to produce a more stable electron configuration.
• Atoms can achieve this stable configuration by forming chemical bonds with other atoms. This
chemical bond can be formed either by gaining or losing an electron(s) (NaCl, MgCl2) or in
some cases due to the sharing of an electron (F2).
• Octet rule.
The atoms having octet configuration, i.e. 8 electrons in the outermost shell, thus symbolize a
stable configuration.
Many of atoms like to have 8 electrons in their outer shell.
There are some exceptions to this rule—the key to remember is to try to get an electron
configuration like a noble gas. Li and Be try to achieve the He electron arrangement

• Only the electrons present in the outer shell, also known as the valence electrons take part in
the formation of chemical bonds.
• Generally, the valency of an element is either equal to the number of dots in the corresponding
Lewis symbol or 8 minus the number of dots (or valence electrons).
 Types of Chemical Bonds
• The type of chemical bonds formed vary in strength and properties.
• There are 4 primary types of chemical bonds which are formed by
atoms or molecules to yield compounds. These types of chemical
bonds include:
1. Ionic Bonds
2. Covalent Bonds
3. Hydrogen Bonds
4. Van der waals interaction

• These types of bonds in chemical bonding are formed from the loss,
gain, or sharing of electrons between two atoms/molecules.
 Types of Chemical Bonds
• The type of chemical bonds formed vary in strength and properties.
• There are different types of chemical bonding possible between atoms
which make the molecules. Types of bonding that are considered to
exist in molecules are categorized as shown below.

• These types of bonds in chemical bonding are formed from the loss,
gain, or sharing of electrons between two atoms or molecules.
 Introduction to Chemical Bonds
• Valance electrons are the electrons that form the outermost
shell of an atom.
 Introduction to Chemical Bonds
• A common atom contains a nucleus composed of protons
and neutrons, with electrons in certain energy levels
revolving around the nucleus.

• Elements are distinguishable from each other due to their

"electron cloud," or the area where electrons move around
the nucleus of an atom.

• In chemical bonding, only valence electrons, electrons

located in the orbitals of the outermost energy level
(valence shell) of an element, are involved.
 Ionic Bonds
• An ionic bond is a chemical bond formed by the electrostatic
attraction between positive and negative ions. The bond is
formed between two atoms when one or more electrons
are transferred from the valence shell of one atom to the
valence shell of the other atom.
 Ionic Bonds
• Ionic bonding is a type of chemical bonding which involves a transfer of
electrons from one atom or molecule to another.
• Here, an atom loses an electron which is in turn gained by another atom.
When such an electron transfer takes place, one of the atoms develops a
negative charge and is now called the anion.

• The other atom develops a positive charge and is called the cation. The ionic
bond gains strength from the difference in charge between the two atoms,
i.e. the greater the charge disparity between the cation and the anion, the
stronger the ionic bond.
 Formation of Sodium Chloride (NaCl)
• The atomic number of Sodium is 11 and its electronic configuration is 2, 8, 1. It has one
electron excess to the nearest stable electronic configuration of a noble gas - Neon. So sodium
has a tendency to lose one electron from its outermost shell and acquire a stable electronic
configuration forming sodium cation (Na+).
• Electron atomic number of chlorine is 17 and its electronic configuration is 2, 8, 7. It has one
electron less to the nearest stable electronic configuration of a noble gas - Argon. So chlorine
has a tendency to gain one electron to acquire a stable electronic configuration forming
chloride anion (Cl−).

• When an atom of sodium combines with an atom of chlorine, an electron is transferred from
sodium atom to chlorine atom forming sodium chloride molecule thus both the atoms achieve
stable octet electronic configuration.
 Formation of Magnesium Chloride (MgCl2)
• The atomic number of Magnesium is 12 and the electronic configuration is 2,
8, 2. It has two electron excess to the nearest stable electronic configuration
of a noble gas - Neon. So magnesium has a tendency to lose two electrons
from its outermost shell and acquire a stable electronic configuration forming
magnesium cation (Mg2+).

• As explained earlier two chlorine atoms will gain two electrons lost by the
magnesium atom forming magnesium chloride molecule (MgCl2)
 Covalent Bonds
• A covalent bond indicates the sharing of electrons between atoms.
Compounds that contain carbon (also called organic compounds)
commonly exhibit this type of chemical bonding.

• The pair of electrons which are shared by the two atoms now extend
around the nuclei of atoms, leading to the creation of a molecule.
 Single and multiple Covalent Bonds
• The number of pairs of electrons shared between two atoms
determines the type of the covalent bond formed between them.

• When more than one pair of electrons are shared between atoms
multiple covalent bonds form. These can be double or triple
bonds depending on the number of pairs of electrons shared
 Formation of single bond in hydrogen (H2) molecule
• Hydrogen molecule is formed by two hydrogen atoms. Each having one
valence electron (1s1), it is contributed to the shared pair and both
atoms acquire stable completely filled electronic configuration.

• Two hydrogen atoms are connected by a covalent bond. This can be

represented by two dots or a single bar.
 Formation of single bond chlorine (Cl2) molecule
• Chlorine molecule is formed by two chlorine atoms. Each chlorine
atom has seven valence electrons (2,8,7). These two atoms achieve a
completely stable electronic configuration (octet) by sharing a pair of
electrons.
 Formation of double bond Ethane (C2H4) molecule
• A double covalent bond is a covalent bond formed by atoms that share
two pairs of electrons.

• The double covalent bond that occurs between the two carbon atoms
in ethane can also be represented by a structural formula and with a
molecular model as shown above.
 Formation of triple bond in nitrogen (N2) molecule
• Nitrogen molecule is formed by two nitrogen atoms. Each nitrogen
atom has five valence electrons (2, 5). These two atoms achieve a stable
completely filled electronic configuration (octet) by sharing three pair
of electrons. Hence a triple bond is formed in between the two atoms.
 Polarity and Covalent Bonds
• Covalent bonds can be either be Polar or Non-Polar in nature.
• Polarity is the competing forces between two atoms for the electrons.

• A molecule is polar when the electrons are attracted to a more

electronegative atom due to its greater electron affinity.
 Polarity and Covalent Bonds
• Covalent bonds can have ionic characteristics.
 Electronegativity and Bond polarity
• Electronegativity (EN): the ability of an atom to attract the shared
electrons in a covalent bond. It determines how the shared electrons are
distributed between the two atoms in a bond.

• The more strongly an atom attracts the electrons in its bonds, the larger its
electronegativity.
• Metals on left side of periodic table attract electrons weakly, thus lower EN.
• Halogens and other reactive nonmetals on right side of periodic table
attract electrons strongly, higher electronegativities
 Electronegativity and Bond Polarity
• One way to figure out what type of bond a molecule has is by determining
the difference of the electronegativity values of the molecules.

• Differences in electronegativity produce bond polarity

If the difference is between 0.0-0.4, then the molecule has a non-polar bond.
If the difference is between 0.4-1.8, then the molecule has a polar bond.
If the difference is 1.8 or more, then the molecule has an ionic bond.
 Electronegativity Bond Polarity
• Electrons in a polar covalent bond are shifted toward the more
electronegative atom; thus, the more electronegative atom is the one
with the partial negative charge.

• In HCl polar covalent bond, the electronegativity values of H and Cl

are 2.1 and 3.0 respectively. i.e. the electronegativity difference is 0.9.
Due to electronegativity difference between H and Cl, H gained partial
positive charge and Cl gained partial negative charge.
 Polar Covalent Bonds
• Polar covalent bonds form when the electrons are not shared
equally between two atoms, causing there to be a partial positive charge
(δ+) and a partial negative charge (δ-) on the atoms (otherwise known as
a dipole moment)

• This occurs when the electronegativities of the two atoms are not equal,
causing the more electronegative atom to “steal” the electrons from the
other atom.
 Polar Covalent Bonds in Water (H2O) molecule
• In a water molecule (above), the bond connecting the oxygen to each
hydrogen is a polar bond.

• Oxygen is a much more electronegative atom than hydrogen,

meaning that it attracts shared electrons more strongly, so the oxygen of
water bears a partial negative charge (has high electron density),
while the hydrogens bear partial positive charges (have low
electron density).
• Since H and O atoms have different electronegativity. (H=2.1,
O=3.5)the water is a polar molecule.
 Non-polar Covalent Bonds
• A non-polar covalent bond is a covalent bond in which the bonding
electrons are shared equally between the two atoms.
• Since the electron pair is shared equally, the partially positive and the
partially negative charges cancel out, causing there to be no partial
charges on the molecule.

• In a non-polar covalent bond, the distribution of electrical charge is

balanced between the two atoms.
 Non-polar Covalent Bonds
• In a nonpolar covalent bond, the electrons are evenly distributed. Non-
polar molecules are formed when atoms have the same or similar
electronegativity.

• In general, if the electronegativity difference between two atoms is zero

less than 0.4, the bond is considered non-polar, even though the only
truly non-polar molecules are those formed with identical atoms.
 Non-polar Covalent Bonds
• Examples of homonuclear non-polar molecules are hydrogen (H2),
oxygen (O2), chlorine (Cl2) and nitrogen (N2).
 Non-polar Covalent Bonds
• Examples of other nonpolar molecules include carbon dioxide (CO2)
and the organic molecules methane (CH4), Carbon tetrachloride (CCl4)
and Benzene (C6H6). Most carbon compounds are nonpolar.
• The effects of the local dipoles cancel each other

• Although carbon and hydrogen do not have exactly the same

electronegativity, they are quite similar, so carbon-hydrogen bonds are
considered non-polar.
 Hydrogen Bonds
• It is a type of polar covalent bonding between oxygen and hydrogen
wherein the hydrogen develops a partial positive charge. This implies
that the electrons are pulled closer to the more electronegative
oxygen atom.

• Compared to ionic and covalent bonding, Hydrogen bonding is a

weaker form of chemical bonding.
• Most important noncovalent interaction in biological molecules.
 Hydrogen Bonds between Water Molecules
• In water molecules during the formation hydrogen bonding, electrons
are pulled closer to the more electronegative oxygen atom.

• This creates a tendency for the positively charged hydrogen to be

attracted towards the negative charges of any neighbouring atom.
• Hydrogen bonding in water contributes to its unique properties,
including its high boiling point (100 °C) and surface tension.
 Importance of Hydrogen Bonds in molecules
• Hydrogen bonds occur in inorganic molecules, such as water, and
organic molecules, such as DNA and proteins.
• Intramolecular hydrogen bonding is partly responsible for folding and
shaping in proteins and nucleic acids.
 Importance of Hydrogen Bonds in molecules
• The two complementary strands of DNA are held together by
hydrogen bonds between complementary nucleotides (A-T and C-G).

• The hydrogen bonds help the proteins and nucleic acids form and
maintain specific shapes.
 Hydrophobic and Hydrophilic interactions
• Hydrophobic and hydrophilic interactions are two major
intermolecular forces between hydrophobic nonpolar and hydrophilic
polar sites of macromolecules or materials surfaces in solvents.
• A hydrophobic substance is one that has a weak or no affinity to
water. Examples of hydrophobic substances include oils, fats, and other
greasy substances.
• A hydrophilic substance is one that has a strong affinity toward
water. Examples of hydrophilic substances include sugars, salts, vinegar,
and many amino acids.
• Hydrophobic interactions are relatively stronger than other weak
intermolecular forces (i.e., Van der Waals interactions or Hydrogen
bonds).
 Hydrophobic interactions
• Hydrophobic interactions describe the relations between water
and hydrophobes (low water-soluble molecules). Hydrophobes are nonpolar
molecules and usually have a long chain of carbons that do not interact with
water molecules.

• The mixing of fat and water is a good example of this particular interaction.
 Biological Importance of Hydrophobic Interactions
• Hydrophobic Interactions are important for the folding of proteins. This is
important in keeping a protein stable and biologically active, because it
allows the protein to decrease in surface area and reduce the undesirable
interactions with water.

• Besides from proteins, there are many other biological substances that rely
on hydrophobic interactions for its survival and functions, like the
phospholipid bilayer membranes in every cell of your body.
 Hydrophilic interactions
• A hydrophobic substance is one that has a weak or no affinity to water.
Examples of hydrophobic substances include oils, fats, and other greasy
substances.
• A hydrophilic substance is one that has a strong affinity toward water.
Examples of hydrophilic substances include sugars, salts, vinegar, and
many amino acids.

• Hydrophobic interactions can hold together non-polar portions of

molecules that have been pushed aside by linked groups of water
molecules.
 Van der Waals interactions
• Van der Waals interactions are weak attractions or interactions
between molecules.All compounds exhibit van der Waals forces.

• The forces are named for the Dutch physicist Johannes Diderik van
der Waals, who in 1873 first postulated these intermolecular forces
in developing a theory to account for the properties of real gases.

• Van der Waals attractions can occur between any two or more
molecules and are dependent on slight fluctuations of the electron
densities, which are not always symmetrical around an atom.

• For these attractions to happen, the molecules need to be very

close to one another.
 van der Waals interactions
• Van der Waals interactions are weak attractions or
interactions between molecules.
• Van der Waals attractions can occur between any two or
more molecules and are dependent on slight fluctuations of
the electron densities, which are not always symmetrical
around an atom.
• For these attractions to happen, the molecules need to be
very close to one another.
• These bonds—along with ionic, covalent, and hydrogen
bonds—contribute to the three-dimensional structure of
proteins that is necessary for their proper function.
 Van der Waals interactions
• Van Der Waals Bonding - Although atoms are electrically NEUTRAL,
the electrons within them are in a constant state of motion, and so
may MOMENTARILY form small electric DIPOLES.
 Van der Waals interactions
• The basis of a van der Waals interaction is that the distribution of
electronic charge around an atom changes with time.
• At any instant, the charge distribution is not perfectly symmetric.
This transient asymmetry in the electronic charge around an atom
acts through electrostatic interactions to induce a complementary
asymmetry in the electron distribution around its neighboring atoms.
 Van der Waals interactions
• The surface area of a molecule determines the strength of the van
der Waals interactions between molecules. The larger the surface
area, the larger the attractive force between two molecules, and the
stronger the intermolecular forces.
 van der Waals interactions
• Occur between all neighboring molecules and arise because
the electron distribution within molecules that are
constantly changing
 van der Waals interactions
• These bonds—along with ionic, covalent, and hydrogen
bonds—contribute to the three-dimensional structure of
proteins that is necessary for their proper function.
 Functional Groups
• A functional group is a specific group of atoms or bonds within a
compound that are most commonly involved in chemical reactions.
• They give physical and chemical properties to the compounds to which
they attach.
 The Roles of Functional Groups
They give physical and chemical properties to the compounds to which
they attach.

Functional groups play a significant role in directing and controlling

organic reactions.

Functional groups also play an important part in organic compound

nomenclature; combining the names of the functional groups with the
names of the parent alkanes provides a way to distinguish compounds.

Functional groups can be used to distinguish similar compounds from

each other.
 Types of functional Groups
• Many biologically active biomolecules contain one or more functional
groups. Some of the important functional groups in biological molecules
include: hydroxyl, methyl, carbonyl (aldehyde and ketone), carboxyl, amino
and phosphate groups.
 Hydroxyl R-OH
• A hydroxyl (alcohol group) is an –OH group covalently bonded to a carbon atom.
• The oxygen atom is much more electronegative than either the hydrogen or the
carbon, which will cause the electrons in the covalent bonds to spend more time
around the oxygen than around the C or H.
Structure

• Therefore, the O-H and O-C bonds in the hydroxyl group will be polar covalent
bonds. The figure above shows the partial charges δ+ and δ- associated with
hydroxyl group.
 Importance of Hydroxyl R-OH group
• Alcohols are organic compounds in which the hydroxyl functional
group (-OH) is bound to a carbon atom.

• Alcohols are an important class of molecules with many scientific,

medical, and industrial uses.
 Methyl R-CH3
• The methyl group consists of a carbon atom bound to 3 hydrogen
atoms. The methyl group is the non-polar functional group. The methyl
groups are unable to form hydrogen bonds and will not interact with
polar compounds such as water.
Structure

• The methyl groups are found in a variety of biologically relevant

compounds.
 Methyl R-CH3
• The methyl groups highlighted below are found in a variety of
biologically relevant compounds.
 Amino R-NH2
• The amino group consists of a nitrogen atom attached by single bonds
to hydrogen atoms. An organic compound that contains an amino
group is called an amine.
Structure

• At the pH of most biological systems, amino group accept H+ become

charged (R-NH3+). Since amino groups can remove H+ from solution,
they are considered basic.
 Amide R-(C=O)NH2
• The amide functional group has an nitrogen atom attached to a
carbonyl carbon atom.
Structure
 Carbonyl R-(C=O)-R’
• A carbonyl group is a chemically organic functional group composed of
a carbon atom double-bonded to an oxygen atom --> [C=O].
Structure

• The simplest carbonyl groups are aldehydes and ketones usually

attached to another carbon compound. These structures can be found
in many aromatic compounds contributing to smell and taste.
 Carbonyl R-(C=O)-R’
• The simplest carbonyl groups are aldehydes and ketones usually
attached to another carbon compound.
Structures

Aldehyde Ketone

• These structures can be found in many aromatic compounds

contributing to smell and taste.
 Aldehyde R-CHO
• An aldehyde is an organic compound that contains a carbonyl group
with the central carbon bonded to a hydrogen and R group (R-CHO).

• Aldehydes differ from ketones in that the carbonyl is placed at the end
of the carbon skeleton rather than between two carbon atoms of the
backbone.
 Ketones RC(=O)R’
• When a carbonyl functional group is placed within a molecule, it is known as
a ketone. Ketones are organic compounds with the structure RC(=O)R’,
where R and R’ can be a variety of carbon-containing substituents.
 Carboxyl R-COOH
• Carboxylic acid is a combination of a carbonyl group and a hydroxyl
group attached to the same carbon, resulting in new characteristics.
Structure

• The carboxyl group can ionize, which means it can act as an acid and
release the hydrogen atom from the hydroxyl group as a free proton
(H+).
 Carboxylate RCOO-
• A carboxylate ion is the conjugate base of a carboxylic acid.
Structure

• Carboxylate ions are the conjugate bases of carboxylic acids, ie. the
deprotonated carboxylic acid. Carboxylate ions can be shown in text
as: RCOO-.
 Carboxylate RCOO-
• A carboxylate ion is the conjugate base of a carboxylic acid.
 Phosphate R-PO4
• A phosphate group is an phosphorus atom covalently bound to 4
oxygen atoms and contains one P=O bond and three P-O− bonds.
Structure

• At the pH of most biological systems, phosphate group release H+

become charged (forms R-OPO32-). Since phosphate groups can release
H+ into solution, they are considered acidic.
 Importance of a Phosphate R-PO4 Group
• The phosphate group is important in living things in different ways.
It is an important structural component of nucleotide, which is the basic
structural unit of DNA and RNA.
It is also a part of the hydrophilic head of phospholipids in biological
membrane.
It is a component of energy-rich molecules, such as ATP.

Nucleotide Phospholipid Adenosine Triphosphate (ATP)

END OF LECTURE
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